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  • Re: 225G Preliminary Worldwide Tracking & Evaluation

    Almost twice as many females have it than males.
    Only 3 over 40 have it (1 age unknown)

    A/Catalonia/NS7362/2009 11-26-09 00 M (TR )
    A/Catalonia/S1096/2009 07-14-09 11 M
    A/Catalonia/S1162/2009 07-28-09 05 M
    A/Catalonia/S1179/2009 07-30-09 24 F
    A/Catalonia/S1181/2009 07-30-09 23 F
    A/Catalonia/S1267/2009 08-24-09 04 F
    A/Catalonia/S1268/2009 08-24-09 08 F
    A/Catalonia/S1402/2009 09-22-09 05 F
    A/Catalonia/S1501/2009 10-08-09 09 F
    A/Catalonia/S1687/2009 11-03-09 04 F
    A/Catalonia/S1748/2009 11-09-09 41 M
    A/Catalonia/S1751/2009 11-09-09 13 F
    A/Catalonia/S1761/2009 11-09-09 49 M
    A/Catalonia/S1827/2009 11-13-09 60 F
    The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

    Comment


    • Re: 225G Preliminary Worldwide Tracking & Evaluation

      via NS1 -

      Rio5826 with 225G also carries the syn413K like the Ukraine and Spain. No NA is available to verify cross-link.
      Rio5090 has a strange coding at 190 (mixed signal), very strange. As you know, some consider 190 an antigenic area and a virulence marker.

      Comment


      • Re: 225G Preliminary Worldwide Tracking & Evaluation

        A/India/8489/2009 at GISAID collected Oct 20.
        Twitter: @RonanKelly13
        The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

        Comment


        • Re: 225G Preliminary Worldwide Tracking & Evaluation

          In spite of what may be written elsewhere, around Oct 20 was a period of lower flu activity and less fatalities. It took 2 more weeks and the onset of winter for the number of cases to rise, fatalities started to rise 2 weeks after that again. The winter waves are most significant in Northern India, in areas that were little affected by the Summer wave.
          Cases:
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          Fatalities:
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          See http://www.flutrackers.com/forum/sho...=111798&page=6
          and http://www.flutrackers.com/forum/sho...=123501&page=2 for further details of H1N1 in India.
          Last edited by Ronan Kelly; January 12, 2010, 04:22 PM. Reason: added graph titles
          Twitter: @RonanKelly13
          The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

          Comment


          • Re: 225G Preliminary Worldwide Tracking & Evaluation

            Originally posted by sharon sanders View Post
            2010-01-01

            HA syn413K and NA syn407V Cross Segment Linkage Increases Range and Penetration

            Cross-Linked Silent HA and NA Polymorphisms Correlated with Fatal 225G Cases in the Ukraine and Russia
            • HA:syn413K encoded from A1281G, AAa->AAg
            • NA:syn407V encoded from T1221C, GTt->GTc

            PF11 Sequences Demonstrating Cross Segment Linkage
            • Ukraine Kyiv377 with mixture of 225D, 225G, 225N, 225S, 225T and 225A
            • Ukraine Lviv673
            • Ukraine Lviv682
            • Ukraine Cherkasy332 *
            • Ukraine Cherkasy333 *
            • Ukraine Cherkasy346 *
            • Ukraine Dnipropetrovsk260 *
            • Ukraine Dnipropetrovsk267 *
            • Ukraine Dnipropetrovsk268 *
            • Ukraine Dnipropetrovsk272 *
            • Ukraine Dnipropetrovsk273 with mixture of wt 225D and 225G *
            • Ukraine Dnipropetrovsk274 *
            • Ukraine Dnipropetrovsk1124 *
            • Ukraine Dnipropetrovsk1171 *
            • Ukraine LvivN2
            • Ukraine LvivN6
            • Ukraine TernopilN10
            • Ukraine TernopilN11
            • MoldovaG120 *
            • MoldovaG140 *
            • MoldovaG181 *
            • MoldovaG182 *
            • MoldovaG191 *
            • HA and NA Norway2924 with mixture of wt 225D and 225G
            • HA and NA Norway3364-2
            • HA and NA CatNS7362 TamiFlu Resistant
            • HA and NA CatS1096
            • HA and NA CatS1162
            • HA and NA CatS1179
            • HA and NA CatS1181
            • HA and NA CatS1267
            • HA and NA CatS1268
            • HA and NA CatS1402
            • HA and NA CatS1501
            • HA and NA CatS1687
            • HA and NA CatS1748
            • HA and NA CatS1751
            • HA and NA CatS1761
            • HA and NA CatS1827
            • HA and NA CatS1935 *
            • HA and NA Guangdong02
            • HA and NA Guangdong05
            • HA and NA SingaporeON1156
            • HA and NA Stockholm31
            • HA and NA Russia14
            • HA and NA Russia19
            • HA and NA Russia74
            • HA and NA Russia165
            • HA and NA Russia178
            • HA and NA Russia190
            • HA and NA Russia191
            • HA and NA Omsk02
            • HA and NA Tver2969 with 225G, Fatal outcome *
            • HA and NA Salekhard01 with 225G, presumptive Fatal outcome
            • HA and NA Orenburg2974 with 225N, potential Fatal outcome
            • HA and NA NY3702
            • HA and NA NY3715
            • HA and NA NY3828
            • HA and NA RhodeIsland08
            • HA and NA Texas42102708
            • HA and NA Texas45072128
            • HA and NA Texas45122886
            • US Private Sequence TamiFlu Resistant

            63 sequences have encircled the globe as of 2010-01-13 * with high fidelity carrying a cross-segment paired set of background markers matching and potentially contributing to the Ukraine fatal cases. Kyiv377 from early November in the Ukraine demonstrates a level of hyper-morphic behaviour at amino acid 225 that is previously undocumented in ΣPF11, but is the natural progression of the genetic acquisition trend line on this pandemic reservoir. Two sequences now additionally demonstrate the TamiFlu Resistant 275Y on NA, one from Spain in late November 2009 and one from the US with details stored in a private database.

            Moldova, a neighbor of the Ukraine, demonstrates extensive NA syn407V, but is missing the HA area for the syn413K on most sequences. 5 of 7 from Moldova with complete HA sequences display the cross segment linkage.

            Expect to see many sequences from the Ukraine on this particular background when HA and NA are deposited for review as most of the recent published Hemagglutinins do carry the syn413K and the published Neuraminidase match the syn407V. Chernihiv452 from the Ukraine with a mixture of 225D, 225G, 225N and 225S carries the syn413K, but has no NA published. A more comprehensive deposit of these two antigenic gene segments (HA and NA) from the Ukraine would allow a definitive conclusion.

            Areas covered include Texas (3), the Northeastern United States (4), China (2), Singapore, the Ukraine (18), Moldova (5), Russia (11), Norway (2), Sweden and extensive penetration in Spain (15 sequences). This particular background pattern may precurse 225G and mixtures of 225D / 225G. If LvivN6 is officially confirmed as a vaccine escape event, these cross-segment pairs may be surveilled as potential future effectors of vaccine efficacy failure.

            Publication of the remaining Neuraminidase segments for the 33 Norwegian and Japanese specimens bearing HA syn413K would allow a more precise review. Although 9 of the recent sequences from Norway carry syn413K, none of the 225E strains from Norway have the syn413K. The patterns are highly suggestive that all of the Norse 225G strains do. The 2009-12-29 release of the NA for Norway2924 confirmed that previous suggestion.

            The Orenburg2974 sequence from Russia also carries 225N on this background. Bryansk2971, also from Russia with presumably fatal 225G from the lung, demonstrates the syn413K but has no entry for the Neuraminidase to confirm this cross segment linkage.

            If RBS revisions at amino acid 225 are, in fact, instructive of high pathogenicity, then Russia is in the FlightPath for a more virulent winter and the Ukraine has presently built a fog of miasma that appears to be capable of spreading across the globe.

            Added Ukraine from today, 100% of sequences with HA and NA are on the cross-segment linkage background. 18 HA have syn413K and 11 NA have syn407V.

            Added Tver from Russia, 225G and fatal.

            Comment


            • Re: 225G Preliminary Worldwide Tracking & Evaluation

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              Twitter: @RonanKelly13
              The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

              Comment


              • Re: 225G Preliminary Worldwide Tracking & Evaluation

                Using the above figures, it seems that a patient infected with the D225G mutation is 3-4 times more likely to have a fatal outcome.
                Twitter: @RonanKelly13
                The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

                Comment


                • Re: 225G Preliminary Worldwide Tracking & Evaluation

                  the text is .pdf-protected so that we can't easily quote from it or easily copy it.
                  I assume that means it is not determined for the general public, the press ?!

                  ...strongly suggesting D222G occurred sporadically...
                  ... prevalence of D225G is less than 1.8% (52 out of 2755).
                  Of 364 fatal cases ...26 (7.1%) had the D222G
                  Atlanta found D222G in 14 samples (out of ?) but not in the original specimens
                  indicating that it occured after growth in the lab.

                  ------------------------------------

                  it seems to be more prevalent in Ukraine,Norway,Spain,Russia.
                  (how many of the 52 ?)
                  So is this a genetical background, that it occurs more
                  often together with other mutations, or is it connected
                  to other things special to these countries (and their lab.
                  growth methods ?) or to those
                  test more for it or is it just coincidence ?
                  I'm interested in expert panflu damage estimates
                  my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                  Comment


                  • Re: 225G Preliminary Worldwide Tracking & Evaluation

                    The original .pdf isn't protected, it's just the way RoRo posted it that doesn't allow cut/pasting.

                    Here are the important points that (IMO) need to be repeated:

                    1. These substitutions in HA and/or PB2 have been reported in viruses obtained from mild to severe to fatal illness case but such viruses have neither formed distinct phylogenetic clusterings nor been associated with consistent changes in virus antigenicity.

                    2. These changes have been found since April 2009 but not been associated with temporal or geographical clustering, strongly suggesting the mutation in these viruses have occurred sporadically as opposed to the emergence and sustained transmission of a variant virus.

                    3. Surveillance and laboratory analysis efforts to study this substitution have given priority to specimens from hospitalized and severely ill patients, leading to potential biases in the data.

                    4. A study done by the WHO Collaborating Centres for Reference and Research on Influenza (WHOCC) in Atlanta located in the Centers for Disease Control and Prevention (CDC) found the D222G substitution in 14 virus isolates but not in viruses in the original clinical specimens indicating the D222G substitution in these 14 virus isolates occurred after growth in the laboratory.

                    5. Otherwise, the pandemic (H1N1) 2009 viruses with D222G substitution have been antigenically similar to the A/California/7/2009 (H1N1) virus, the WHO‐recommended vaccine virus.
                    The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                    Comment


                    • Re: 225G Preliminary Worldwide Tracking & Evaluation

                      Sorry Gs, I posted as a jpeg not a text file. I would be interested to hear both your opinions of the higher frequency of the D225G mutations in fatal cases. Am I correct in thinking that this mutation allows the virus to attack deep lung tissue? If so, more severe illness could be a consequence and not necessarily a bias.
                      My own feeling is that the mutation gives rise to a greater likelyhood of severe and fatal outcomes by a factor of 3-4. The latest CDC estimates give an overall cfr of 0.02% (11,160 fatalities from 55 million cases). So the mutation could raise the cfr to something approaching seasonal flu. Whether or not that becomes significant in the long run depends on transmissability of the mutation.
                      I think that the number to watch is that 1.8% number. If that goes up it would suggest that the mutation is spreading and there could be a significant (but not apocalyptic) rise in overall cfr.
                      Last edited by Ronan Kelly; January 16, 2010, 08:58 AM. Reason: typo
                      Twitter: @RonanKelly13
                      The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

                      Comment


                      • Re: 225G Preliminary Worldwide Tracking & Evaluation

                        RoRo,
                        This is my non-scientific personal opinion. I've read quite a few analyses of the 225 mutations and I'm going with what I believe to be true, which are the official ones.

                        1. & 2. I think are true. Notice the dates and the locations. The degree of severity is not listed but we know they were still testing mild cases in the spring and early summer.
                        Here is a list of sequences with 225G (or mixed)

                        C:\gs>travel1 mxha6 716
                        G >A/Mexico/InDRE4114/2009
                        G >A/Mexico/InDRE4114/2009
                        R >A/Texas/42291877/2009
                        G >A/Vladivostok/01/2009
                        R >A/Nebraska/02/2009/04
                        G >A/NY/04/2009/04
                        G >A/Mexico/3955/2009/04/02
                        R >A/CA/07/2009/04/09
                        R >A/Texas/04/2009/04/14
                        G >A/Texas/05/2009/04/15
                        R >A/CA/13/2009/04/21
                        R >A/Texas/10/2009/04/23
                        G >A/Texas/11/2009/04/23
                        R >A/NY/31/2009/04/24
                        R >A/NY/11/2009/04/25
                        G >A/Georgia/01/2009/04/27
                        T >A/Sw/Alberta/OTH-33-3/2009/05/03
                        G >A/Hiroshima/201/2009/06/17
                        G >A/Sao Paulo/53206/2009/07/19
                        R >A/Finland/614/2009/07/24
                        G >A/Utah/42/2009/07/24
                        R >A/Utah/42/2009/07/24
                        G >A/Catalonia/NS1706/2009/07/29
                        N >A/Singapore/GP2312/2009/07/31
                        G >A/Sao Paulo/53225/2009/08/01
                        G >A/Catalonia/NS2001/2009/08/03
                        G >A/Catalonia/NS2008/2009/08/03
                        N >A/Singapore/GP2641/2009/08/05
                        N >A/Singapore/GP2651/2009/08/05
                        R >A/Norway/2924/2009/08/10
                        G >A/Norway/3206-3/2009/09/01
                        G >A/Zhejiang-Yiwu/11/2009/09/06
                        G >A/Zhejiang/DTID-ZJU02/2009/09/07
                        G >A/Zhejiang/DTID-ZJU03/2009/09/07
                        34 -:121 A:1751 G:19 N:3 R:11 T:1

                        3. I think they are concerned and now are specifically studying these mutations; so we can expect to see more sequences with them. Either I missed discussions on mutation K340N or no one has been paying attention; but they are now, so I think we can expect to see more with this one, too.

                        4. We recently saw a study linking this mutation to passage in eggs.

                        5. The only thing I know about this is I see this notation occassionally in the sequence comments.
                        The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                        Comment


                        • Re: 225G Preliminary Worldwide Tracking & Evaluation

                          Originally posted by mixin View Post
                          The original .pdf isn't protected, it's just the way RoRo posted it that doesn't allow cut/pasting.

                          Here are the important points that (IMO) need to be repeated:

                          1. These substitutions in HA and/or PB2 have been reported in viruses obtained from mild to severe to fatal illness case but such viruses have neither formed distinct phylogenetic clusterings nor been associated with consistent changes in virus antigenicity.

                          2. These changes have been found since April 2009 but not been associated with temporal or geographical clustering, strongly suggesting the mutation in these viruses have occurred sporadically as opposed to the emergence and sustained transmission of a variant virus.

                          3. Surveillance and laboratory analysis efforts to study this substitution have given priority to specimens from hospitalized and severely ill patients, leading to potential biases in the data.

                          4. A study done by the WHO Collaborating Centres for Reference and Research on Influenza (WHOCC) in Atlanta located in the Centers for Disease Control and Prevention (CDC) found the D222G substitution in 14 virus isolates but not in viruses in the original clinical specimens indicating the D222G substitution in these 14 virus isolates occurred after growth in the laboratory.

                          5. Otherwise, the pandemic (H1N1) 2009 viruses with D222G substitution have been antigenically similar to the A/California/7/2009 (H1N1) virus, the WHO‐recommended vaccine virus.
                          Very nice Mixin.

                          Beautifully succinct and, for me , right on the money.

                          Comment


                          • Re: 225G Preliminary Worldwide Tracking & Evaluation

                            comment via email from NS1 -


                            The three recent Iraqi sequences at GISAID all carry the cross segment linkage on both the HA and NA. This precursor background to 225G is widespread and is penetrating.

                            Iraq/8529E3 2009-09-08
                            Iraq/8529M1 2009-09-08
                            Iraq/8531 2009-09-08

                            This background may correlate with hyper-morphic behaviour at antigenic sites additional to the RBD. Among the three published sequences from two samples in Iraq, we find the following HA polymorphisms that revise the amino acid, including the 298V predicted for the Ukraine and downstream geographies.

                            130E
                            131L (3)
                            160L (2)
                            194I
                            298V (3)

                            A synonymous 419L is carried onto all Iraq sequences, a change previously found on the Utah42 sequence that carried 225G. The syn419L (CTg=>CTa) does not seem to appear previously in PF11 outside these 4 mentioned sequences. The progenitor is unknown at this time though circumstantial evidence suggests H7 or H2 Avian potential (perhaps production poultry or an undocumented desert bird infected from migratory waterfowl).

                            Ten amino acid revisions and three silent changes only found on a single 225G case (Utah42) indicate an acceleration in the genetic acquisition process in Iraq, a country having close intercourse with Russia.

                            Do the cross linked silent changes of HA syn413K and NA syn407V provide a backdrop for hyper-morphic behaviour as the evidence suggests or will we find that randomness is providing the same outcomes in dozens of locations?
                            Last edited by sharon sanders; January 17, 2010, 09:13 PM. Reason: edit via NS1

                            Comment


                            • Re: 225G Preliminary Worldwide Tracking & Evaluation

                              > The progenitor is unknown at this time though circumstantial
                              > evidence suggests H7 or H2 Avian potential (perhaps production
                              > poultry or an undocumented desert bird infected from
                              > migratory waterfowl).

                              lol,
                              migrating waterfowl infecting poultry in the desert
                              and then it goes to humans, mexing with mixflu
                              I'm interested in expert panflu damage estimates
                              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                              Comment


                              • Re: 225G Preliminary Worldwide Tracking & Evaluation

                                Since circumstantial evidence leads us to migratory waterfowl, then I'll add my speculation. Maybe they saw the huge pig sewage pools and thought they were lakes.. and stopped by for a bit... leaving their bird flu infected droppings. Then the thousands of flies (that the people complained about) walked through/fed on the infected droppings, then carried the virus into homes.
                                The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                                Comment

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